Search results for " math"
showing 10 items of 11183 documents
Hierarchical log Gaussian Cox process for regeneration in uneven-aged forests
2021
We propose a hierarchical log Gaussian Cox process (LGCP) for point patterns, where a set of points x affects another set of points y but not vice versa. We use the model to investigate the effect of large trees to the locations of seedlings. In the model, every point in x has a parametric influence kernel or signal, which together form an influence field. Conditionally on the parameters, the influence field acts as a spatial covariate in the intensity of the model, and the intensity itself is a non-linear function of the parameters. Points outside the observation window may affect the influence field inside the window. We propose an edge correction to account for this missing data. The par…
Variational Approximations for Generalized Linear Latent Variable Models
2017
Generalized linear latent variable models (GLLVMs) are a powerful class of models for understanding the relationships among multiple, correlated responses. Estimation, however, presents a major challenge, as the marginal likelihood does not possess a closed form for nonnormal responses. We propose a variational approximation (VA) method for estimating GLLVMs. For the common cases of binary, ordinal, and overdispersed count data, we derive fully closed-form approximations to the marginal log-likelihood function in each case. Compared to other methods such as the expectation-maximization algorithm, estimation using VA is fast and straightforward to implement. Predictions of the latent variabl…
Environmental Variability and Semelparity vs. Iteroparity as Life Histories
2002
Research on the evolution of life histories addresses the topic of fitness trade-offs between semelparity (reproducing once in a lifetime) and iteroparity (repeated reproductive bouts per lifetime). Bulmer (1994) derived the relationship v+P(A)<1 (P(A) is the adult survival;vb(S) and b(S) are the offspring numbers for iteroparous and semelparous breeding strategies, respectively), under which a resident semelparous population cannot be invaded by an iteroparous mutant when the underlying population dynamics are stable. We took Bulmer's population dynamics, and added noise in juvenile and adult survival and in offspring numbers. Long-term coexistence of the two strategies is possible in much…
Effects of patch number and dispersal patterns on population dynamics and synchrony.
2000
In this paper, we examine the effects of patch number and different dispersal patterns on dynamics of local populations and on the level of synchrony between them. Local population renewal is governed by the Ricker model and we also consider asymmetrical dispersal as well as the presence of environmental heterogeneity. Our results show that both population dynamics and the level of synchrony differ markedly between two and a larger number of local populations. For two patches different dispersal rules give very versatile dynamics. However, for a larger number of local populations the dynamics are similar irrespective of the dispersal rule. For example, for the parameter values yielding stab…
Spatio-Temporal model structures with shared components for semi-continuous species distribution modelling
2017
Abstract Understanding the spatio-temporal dynamism and environmental relationships of species is essential for the conservation of natural resources. Many spatio-temporally sampled processes result in continuous positive [ 0 , ∞ ) abundance datasets that have many zero values observed in areas that lie outside their optimum niche. In such cases the most common option is to use two-part or hurdle models, which fit independent models and consequently independent environmental effects to occurrence and conditional-to-presence abundance. This may be correct in some cases, but not as much in others where the detection probability is related to the abundance. The aim of this work is to infer the…
Seed Bank in Annuals: Competition Between Banker and Non-banker Morphs
2002
Seed bank is a plant life history strategy against the unpredictability of the biotic and the abiotic environment. We simulated competition between a seed banking and a non-banking morph of an annual plant. A constant fraction of the banker morph seeds was allocated to the seed bank, where they had a constant mortality and germination rate. All surviving seeds of the non-banker morph germinated in the next generation. The seedlings of both morphs experienced similar density-dependent mortality. Whether one of the morphs wins or the morphs coexist was evaluated from parameter space plots and statistically with logistic regression analysis. All parameters of the model had a significant, nonli…
Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium
2010
Abstract Background Synechocystis sp. PCC6803 is a cyanobacterium considered as a candidate photo-biological production platform - an attractive cell factory capable of using CO2 and light as carbon and energy source, respectively. In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network. Results We report the most comprehensive metabolic model of Synechocystis sp. PCC6803 available, iSyn669, which includes 882 reactions, associated with 669 genes, and 790 metabolites. The model includes a detailed biomass equation which encompasses…
An Algebraic Derivation of Chao’s Estimator of the Number of Species in a Community Highlights the Condition Allowing Chao to Deliver Centered Estima…
2014
Anne Chao proposed a very popular, nonparametric estimator of the species richness of a community, on the basis of a limited size sampling of this community. This expression was originally derived on a statistical basis as a lower-bound estimate of the number of missing species in the sample and provides accordingly a minimal threshold for the estimation of the total species richness of the community. Hereafter, we propose an alternative, algebraic derivation of Chao’s estimator, demonstrating thereby that Chao’s formulation may also provide centered estimates (and not only a lower bound threshold), provided that the sampled communities satisfy a specific type of SAD (species abundance dist…
Estimation of local extinction rates when species detectability covaries with extinction probability: is it a problem ?
2006
Estimating the rate of change of the composition of communities is of direct interest to address many fundamental and applied questions in ecology. One methodological problem is that it is hard to detect all the species present in a community. Nichols et al. presented an estimator of the local extinction rate that takes into account species probability of detection, but little information is available on its performance. However, they predicted that if a covariance between species detection probability and local extinction rate exists in a community, the estimator of local extinction rate complement would be positively biased. Here, we show, using simulations over a wide range of parameters…
Incidence and control of black spot syndrome of tiger nut
2017
Tiger nut (Cyperus esculentum) is a very profitable crop in Valencia, Spain, but in the last years, part of the harvested tubers presents black spots in the skin making them unmarketable. Surveys performed in two consecutive years showed that about 10% of the tubers were severely affected by the black spot syndrome whose aetiology is unknown. Disease control procedures based on selection of tubers used as seed (seed tubers) or treatment with hot-water and/or chemicals were assayed in greenhouse. These assays showed that that this syndrome had a negative impact on the germination rate, tuber size and yield. Selection of asymptomatic seed tubers reduced drastically the incidence of the black …